think_barley.rda {PopVar}

An example barley dataset

Description

A sample dataset, previously described in Sallam et al. (2014) is provided as an example of the proper formatting of input files and also for users to become familiar with PopVar; the think_barley dataset is useful in demonstrating both pop.predict and x.val. Note that a number of entries are missing data for one or both traits, which is representative of a real breeding scenario where phenotypic data may not be available for all parent candidates.

Format

The names of the example files are:

G.in_ex

A set of 245 barley lines genotyped with 742 SNP markers

G.in_ex_mat

A n x p matrix of n = 245 barley lines genotyped with p = 742 SNP markers

G.in_ex_imputed

A n x p matrix of n = 245 barley lines and p = 742 imputed SNP marker genotypes

y.in_ex

Phenotypes of four traits for a portion of the 245 barley lines, Fusarium head blight (FHB), deoxynivalenol (DON) in ppm, grain yield in bushels/acre, and plant height in cm.

map.in_ex

Genetic map (i.e. chromosome assignment and genetic distance (cM) between markers) of the 742 SNP markers based on Munoz-Amatriain et al., 2011

cross.tab_ex

A table of user-defined crosses

References

Sallam, A.H., J.B. Endelman, J-L. Jannink, and K.P. Smith. 2015. Assessing Genomic Selection Prediction Accuracy in a Dynamic Barley Breeding Population. Plant Gen. 8(1)